NAME

SPStr - Sphingolipids (SP) structure generation methods

SYNOPSIS

use SPStr;

use SPStr qw(:all);

DESCRIPTION

SPStr module provides these methods:

GenerateCmpdOntologyData - Generate ontology data
GenerateCmpdOntologySDDataLines - Generate ontology data lines for SD file
GenerateSPChainStrData - Generate chain structure data
GenerateSDFile - Generate SD file
GetSPTemplatesData - Get templates data
GetSPSupportedHeadGroupMap - Get supported headgroups data
GetSPTemplateID - Get templates ID
IsSPChainsAbbrevSupported - Is it a supported SP abbreviation
ParseSPAbbrev - Parse SP abbreviation
ProcessSPCmpdAbbrevs - Process SP abbreviation
SetupSPCmpdAbbrevTemplateDataMap - Setup template structure data map
ValidateSPAbbrev - Validate SP abbreviation

METHODS

GenerateCmpdOntologyData: $DataHashRef = GenerateCmpdOntologyData($CmpDataRef);

Return a reference to a hash containing ontology data with hash keys and values corresponding to property names and values.
GenerateCmpdOntologySDDataLines: $DataLinesArrayRef = GenerateCmpdOntologySDDataLines($CmpdDataRef);

Return a reference to an array containing ontology data lines suitable for generate SD file data block.
GenerateSPChainStrData: ($AtomLinesArrayRef, $BondLinesArrayRef) = GenerateSPChainStrData($ChainType, $CmpdDataRef);

Return array references containing atom and bond data lines for SD file. Appropriate atom and bond data lines are generated using chain type and abbreviation template data.
GenerateSDFile: GenerateSDFile($SDFileName, $CmdAbbrevsRef);

Generate a SD file for compound abbreviations. Structure data for specified abbreviation is generated sequentially and written to SD file.
GetSPTemplatesData: $TemplatesDataRef = GetSPTemplatesData();

Return a reference to a hash containing SP templates data
GetSPSupportedHeadGroupMap: $SupportedHeadGroupDataRef = GetSPSupportedHeadGroupMap();

Return a reference to a hash containing supported head groups data.
GetSPTemplateID: $HeadGroupID = GetSPTemplateID($HeadGroupAbbrev, $ChainsAbbrev);

Return a supported template ID for compound abbreviation.
IsSPChainsAbbrevSupported: $Status = IsSPChainsAbbrevSupported($Abbrev, $PrintWarning);

Return 1 or 0 based on whether SP abbreviated is supported. For unsupported SP abbreviations, a warning is printed unless PrintWarning flag is set.
ParseSPAbbrev: ($HeadGroup, $ChainsAbbrev, $AbbrevModifier) = ParseSPAbbrev($Abbrev);

Parse SP abbreviation and return these values: HeadGroup, ChainsAbbrev, AbbrevModifier.
ProcessSPCmpdAbbrevs: ProcessSPCmpdAbbrevs($CmpdAbbrevsRef, $AllowArbitraryChainAbbrev, $WriteSDFile, $SDFileName);

Process specified SP abbreviations to generate structures and write them out either a SD file or simply report number of valid abbreviations.
SetupSPCmpdAbbrevTemplateDataMap: $AbbrevTemplateDataMapRef = SetupSPCmpdAbbrevTemplateDataMap($Abbrev);

Return a reference to a hash containing template data for compound abbreviation. The template data is used to generate SD file for compound abbreviation.
ValidateSPAbbrev: $Status = ValidateSPAbbrev($Abbrev);

Return 1 or 0 based on whether a SP abbreviation is valid.

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy

COPYRIGHT

LICENSE

Modified BSD License